I am trying to compare two genetically different strains that I have sequenced using SOLiD.  I was trying to ask where these two strains are different, either in terms of deletions or polymorphisms, and one idea I had was to use Bowtie to create an index from one of these strains and then to map my reads for the other strain using this index.  Is this a reasonable strategy? <div>
<br></div><div> - Will Light</div><div>   Northwestern University</div>